Hi,
I would like to ask everyone some questions.
I am doing a genome wide screening of siRNA.
At the end of data analysis, I manage to generate the correct data but fail to annotate the wells.
Even though the state is TRUE for annotation but they are not in html report.
State:
configured=TRUE, annotated=TRUE
x <- readPlateList("platelist.txt", name = expName, path=dataPath)
x<-configure(x,confFile = confFile, logFile = logFile,descripFile = desFile, path = dataPath)
x<-annotate(x,geneIDFile="annotationST1.txt",path=dataPath)
xn<-summarizeChannels(x,fun = function (r1,r2,r3,r4,r5,r6,r7) r5/r3)
xnp <- normalizePlates(xn, scale = "multiplicative", log = TRUE, method = "negatives", varianceAdjust = "none")
xsc <- scoreReplicates(xnp, sign = "+", method = "zscore")
xf <- summarizeReplicates(xsc, summary = "mean")
I tried to annotate the x (raw) and xf (summarized) one, but they generated the same results.
Plate Well GeneID
1 A01 DMPK
1 A02 empty
1 A03 TTK
1 A04 PIK3CA
1 A05 SYK
1 A06 KIAA1804
1 A07 EPHA8
1 A08 NAGK
1 A09 empty
1 A10 IRAK1
total 384.
Please someone help me with this.
Thank you.
Hi,
The original script that my supervisor sent me was below:
x <- readPlateList("platelist.txt", name = expName, path=dataPath)
x<-configure(x,confFile = confFile, logFile = logFile,descripFile = desFile, path = dataPath)
#Calculate the survival ratio by normalizing FL channel to the RL
xn<-summarizeChannels(x,fun = function (r1,r2,r3,r4,r5,r6,r7) r5/r3)
#Normalise plates to the median of the plate values
xnp <- normalizePlates(xn, scale = "multiplicative", log = TRUE, method = "negatives", varianceAdjust = "none")
#Score wells within each replicate by caluclating a z score for each well based on replicate median and mad
xsc <- scoreReplicates(xnp, sign = "+", method = "zscore")
#summarize the replicates by taking the mean value for each
xf <- summarizeReplicates(xsc, summary = "mean")
xfw<-annotate(xf,geneIDFile="annotationST1.txt",path=dataPath)
He annotated to xfw variable, which has scores.
In the write report function, the scored input he used was xf.
out <- writeReport(raw=x, normalized=xnp, scored=xf, force = TRUE, plotPlateArgs = TRUE, imageScreenArgs = list(zrange=c( -4, 8),ar=1), map=TRUE, outdir=outPath)
Hence, the Annotated status was FALSE.
However, no matter the annotated status in write report feedback is TRUE or FALSE, the html report generated still no annotations to the wells.
HELP !!!!